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ChangeLog
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ChangeLog
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CHANGES
=======
0.3.0
-----
* fix error in tau-only est
* fix merge error
* added color
* merge
* fix function sig
* estimating tau parameter
* added stuff toestimate tau, a parameter for the population structure in the reference (ie.e how distant the reference is from the admixture source)
* renamed hap arg
* fixed some edge cases
* first testing version, with decoding
* fix logic error with genotypes
* haploid mode testing
* added haploid read emissions and contamination updates
* better setup
* cleanup all
* added profile
* added profiler
* fix assertion in update\_post\_geno
* clean up calculations
* cleanup, moving to numba
* cleanup, moving to numba
* cleanup, moving to numba
* cleanup, moving to numba
* cleanup
* cleanup, some reorganization
* updated figs
* updated notes
* Added posterior decoding
0.2.4
-----
* update with posterior replicates. currently no parameter estimates are performed
0.2.3
-----
* test version for run lenghts using dp
* fixed some edge cases
* test version for run lenghts using dp
* new runs plot
* change rle plot
* broadcast
* scaling emissions
* nan raises error
* cleaning up figs
* removed ALT conflict between altai/alternative
* before plot cleanup
* infer states for rle
* added cli to do run lengths
* fix rle
0.2.2
-----
* rle interface
* some notes on better transition
* added rle output
* added rle
* added check for infile
0.2.1
-----
* bam parsing
* bam parsing
* compatible with py3.5
* py3.5 version
* versioning
* Update admixfrog.tex
* fix python version
* fix python version
* fixed setup requires
* added pbr
* changed req
* bam parsing
* disable cy
* recompiling
* fixed import
* added bam processing
* added pgdirect
* fix imports
* getting pw to run
* build wo cython
* older setuptools
* rules fig
* updated readme
* added docs
* added docs
* moved setup to use pbr
* moved setup to use pbr
* ancestral state might be working
* pipeline
* added vcf to pipeline
* pipeline 1st version
* restore plotting
* pandas version
* clean up plotting
* fast emission
* removed old functions
* setup
* fast betabinomial
* merge
* added update stop
* moved pg to end of loop
* run black
* run black
* posterior calc
* new update functions
* haploid state betabinomial emissions are working, still slow
* some more python functions for betabinomial. still slow
* updated fwd bwd algorihtm. Now uses global gamma (posterior state decoding) variable. Also, initial state removed from there
* clean up before chaning fwd bwd
* emission
* chr1 seems to work, others do not
* mv betabinomial stuff
* cython compiles.
* cython compiles.
* cython compiles.
* cython compiles.
* moved stuff to other files
* betabinomial update
* plotting stuff
* version without X
* added option wo hets, run through black
* fixed underflow issue
* jit remoed memory stuff
* added garbage state
* added garbage state
* added garbage state
* before garbage
* working setup
* deploy
* deploy
* no cython does work again wweee
* no cython doesnt work
* cython still working
* cython still working
* still working, also X/Y
* still working, cython cont est doesnt work
* still working.
* introgression cleaned
* revert 6 states
* working by snp
* Added simple
* init